BACKGROUND: Birth defects are a major public health concern as they are the leading cause of neonatal and infant mortality. Observational studies have linked environmental pollution to adverse birth outcomes, including congenital anomalies. This study examined potential associations between ambient air pollution and congenital heart defects and cleft lip or palate among births in Brisbane, Australia (1998-2004).METHODS: Ambient air pollution levels were averaged over weeks 3-8 of pregnancy among 150,308 births. Using a case-control design, we used conditional logistic regression and matched cases to 5 controls. Analyses were conducted using all births, and then births where the mother resided within 6 and 12 kilometers of an ambient air quality monitor.FINDINGS: When analyzing all births there was no indication that ambient air pollution in Brisbane was associated with a higher risk of cardiac defects. Among births where the mother resided within 6 kilometers of an ambient air quality monitor, a 5 ppb increase in O(3) was associated with an increased risk of pulmonary artery and valve defects (OR 2.96, 95% CI: 1.34, 7.52) while a 0.6 ppb increase in SO(2) was associated with an increased risk of aortic artery and valve defects (OR 10.76, 95% CI: 1.50, 179.8). For oral cleft defects among all births, the only adverse association was between SO(2) and cleft lip with or without cleft palate (OR 1.27, 95% CI: 1.01, 1.62). However, various significant inverse associations were also found between air pollutants and birth defects.CONCLUSIONS: This study found mixed results and it is difficult to conclude whether ambient air pollution in Brisbane has an adverse association with the birth defects examined. Studies using more detailed estimates of air pollution exposure are needed.